Tim Bailey's MEME and MAST programs now have the ability to look for
protein motifs in nucleotide databases. Not exactly findpattern type
searches, but perhaps could be used as such.
http://www.sdsc.edu/MEME
nathan
tjrc1 at mole.bio.cam.ac.uk (Tim Cutts) writes:
>> I am looking for some UNIX pattern matching software, similar to GCG's
> findpatterns, but which will allow me to compare a protein pattern against a
> nucleotide sequence database translated on the fly in all six reading
> frames. Does such a program exist? If not I am willing to try writing
> one, although I can't believe no-one has already done this...
>> Thanks in advance.
>> Tim.
>
--
Nathan Siemers, Ph.D.
Research Investigator, Applied Genomics
Bristol-Myers Squibb Pharmaceutical Research Institute
Visiting Scientist
Whitehead/MIT Center for Genome Research
617-252-1382
siemers at bms.com
